how to maintain headers when piping into samtools

[Kennels]

Hi,

I am using bowtie2 output (which is sam format natively) to pipe into samtools as such:

bowtie2 <all the arguments> | samtools view -S -F 4 -b - | samtools sort - file.sorted

but I am losing the headers when piping.

Is there a way to maintain the headers from bowtie to samtools during the pipe. I can't seem to find an option in samtools view that does this.

thanks

[kcchan]

It works for me when I use -SbF 4 - Not sure why that is, but perhaps -F is stripping out the headers if -b output isn't stated first. You can also use reheader to fix the headers of your already generated files.

[swbarnes2]

use -h in samtools view. That will keep the headers.